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Background The real prevalence and incidence of women living with or at risk of female genital mutilation/cutting (FGM/C) is unknown in Switzerland and many parts of Europe, as there are no representative surveys similar to DHS or MICS for European countries. Indirect estimates are commonly used to estimate the number of women with FGM/C in high-income countries, but may not reflect the actual FGM/C prevalence among migrants. Direct measures may provide more accurate estimates that could guide policy- and clinical decision-making. Swiss hospital data may provide a sample of patients that can be used to describe the prevalence of FGM/C in Swiss hospitals. Our study assesses the number of inpatient women and girls in Swiss university hospitals from countries with high FGM/C prevalence, and of inpatients with a coded diagnosis of FGM/C. Methods We conducted an exploratory descriptive study in Switzerland to assess the number of women and girls admitted to Swiss university hospitals between 2016 and 2018 from 30 FGM/C practicing countries, as well as inpatients with a coded diagnosis of FGM/C using anonymized data. We calculated indirect estimates for inpatient women and girls living with or at risk of FGM/C and compared them with the number of inpatients with a coded diagnosis of FGM/C. Results 8720 women and girls from FGM/C practicing countries were admitted. 207 patients had a coded diagnosis of FGM/C, including 7 with a nationality outside the 30 targeted countries, corresponding to an overall prevalence of 2.3% (95%CI, 2.0–2.6). The number of FGM/C cases by hospital was significantly different across years (P < 0.001), with a higher proportion of cases collected in Geneva, Switzerland. Conclusions The comparison between indirect estimates of inpatients with or at risk of FGM/C and the low number of FGM/C cases coded, suggests low recording and coding capacities of FGM/C. Tweetable abstract The capacity of coding primary and secondary diagnosis of FGM/C in Swiss university hospitals seems low. Protocol number: 2018–01851: SwissEthics Committee, Canton of Geneva, Switzerland.